Extending the models for XX and XO data, so as to keep a consensus network as far as possible.

Steps to find the common link to be added :
1.) Read in the extension.csv for both cell lines
2.) Remove links from TFs and Ligands
3.) Retain only links that have adjusted p-value < 0.001 and value !=0
4.) Calculate %improvement in residual for each cell line
5.) Find the intersection list,(Links that appear in both lists)
6.) Calculate the sum of %improvement in residual
7.) Order the intersection list by descending order of sum of %improvement in residual.
8.) Add the link with Max sum of %improvement to both models.

XX

Initial-Fit

Model residual = 2056

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 178 Gsk3 Igfr 1.41702633999479 1277.72293709044 18 778.578532266446 2 0 0
2 171 Gsk3 Akt 1.99559218209568 1288.71968912995 18 767.581780226938 2 0 0
3 183 Gsk3 Pi3k 15.0727241980515 1289.13219166705 18 767.169277689836 2 0 0
4 176 Gsk3 Fgfr 0.191531955466209 1372.05906755829 18 684.242401798598 2 0 0
5 409 Stat3 Igfr 0.999122672339906 1502.20198472129 17 554.099484635595 1 0 0
6 220 Jak Igfr 0.0556087755678092 1503.11324628534 17 553.18822307155 1 0 0
7 407 Stat3 Fgfr 0.300460094833736 1515.3185437816 17 540.982925575287 1 0 0
8 218 Jak Fgfr 0.0167866219398153 1515.31854382928 17 540.982925527604 1 0 0
9 414 Stat3 Pi3k 6.92522239192528 1519.02257760899 17 537.278891747894 1 0 0
10 225 Jak Pi3k 0.386430781716265 1519.02257765008 17 537.27889170681 1 0 0
11 402 Stat3 Akt 0.536041523286274 1523.34265160666 17 532.958817750223 1 0 0
12 213 Jak Akt 0.0299202958574827 1523.34265280937 17 532.958816547514 1 0 0
13 92 Bmp4r Fgfr 100.000006308235 1854.77449547632 18 201.526973880564 2 0 0
14 29 Actr Fgfr -0.792450311159814 1894.64741080012 17 161.654058556764 1 0 0
15 386 Smad2 Fgfr -2.41665063274279 1894.64741080539 17 161.654058551497 1 0 0
16 8 Activin Fgfr -0.792497812660148 1894.64741081346 17 161.654058543427 1 0 0
17 384 Smad2 Erk -2.2971200884708 1908.4536014253 17 147.847867931582 1 0 0
18 6 Activin Erk -0.753278182588148 1908.45360143937 17 147.847867917512 1 0 0
19 27 Actr Erk -0.753277209074847 1908.45360160677 17 147.847867750115 1 0 0
20 13 Activin Mek -0.179931424708554 1930.52896307738 17 125.77250627951 1 0 0

LA1:Jak -> Fgfr

Model residual = 1515

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 178 Gsk3 Igfr 1.07092508964865 971.812846969374 19 543.189125194063 2 0 0
2 171 Gsk3 Akt 1.68236052914573 980.75472533061 19 534.247246832827 2 0 0
3 183 Gsk3 Pi3k 0.947902586974397 981.104897412239 19 533.897074751199 2 0 0
4 176 Gsk3 Fgfr 0.0366456344380372 1042.9909365935 19 472.011035569937 2 0 0
5 179 Gsk3 Jak 3.57901785216984 1186.00515881884 19 328.996813344597 2 0 0
6 180 Gsk3 Lifr 3.57012904221758 1186.0051592358 19 328.996812927639 2 0 0
7 92 Bmp4r Fgfr 100.000000018277 1379.2932137683 19 135.708758395137 2 0 0
8 96 Bmp4r Lifr 13.860198582644 1405.40002957656 19 109.601942586875 2 0 0
9 95 Bmp4r Jak 10.0003455473115 1405.40002968353 19 109.601942479911 2 0 0
10 90 Bmp4r Erk 0.0999812891114909 1409.88137320982 19 105.120598953621 2 0 0
11 6 Activin Erk -0.615064354135591 1431.0541333998 18 83.9478387636343 1 0 0
12 27 Actr Erk -0.615066582280294 1431.05413356246 18 83.9478386009775 1 0 0
13 384 Smad2 Erk -1.8756670748869 1431.05413414638 18 83.9478380170569 1 0 0
14 97 Bmp4r Mek 0.0950267626764539 1432.52845502105 19 82.4735171423897 2 0 0
15 100 Bmp4r Raf 0.0950267626764539 1432.52845502105 19 82.4735171423897 2 0 0
16 101 Bmp4r Ras 0.0950267626764539 1432.52845502105 19 82.4735171423897 2 0 0
17 409 Stat3 Igfr 41.2673434838526 1435.74300563464 18 79.258966528794 1 0 0
18 220 Jak Igfr 0.368915097530597 1435.74303261254 18 79.2589395508951 1 0 0
19 29 Actr Fgfr -0.183054053565317 1436.60116940405 18 78.4008027593868 1 0 0
20 386 Smad2 Fgfr -0.558216361851173 1436.60116951395 18 78.400802649488 1 0 0

LA2:Gsk3->Igfr

Model residual = 971

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 100.000000000003 841.461666755043 21 129.336847807388 2 0 0
2 90 Bmp4r Erk 10.0000192017944 866.760153279043 21 104.038361283389 2 0 0
3 95 Bmp4r Jak 10.0001269820917 879.28557415186 21 91.5129404105718 2 0 0
4 96 Bmp4r Lifr 214.317017758443 883.773260598781 21 87.0252539636506 2 0 0
5 6 Activin Erk -0.61201399267674 887.232621555181 20 83.5658930072506 1 0 0
6 97 Bmp4r Mek 1.0052953446443 889.238103252294 21 81.5604113101375 2 0 0
7 100 Bmp4r Raf 1.0052953446443 889.238103252294 21 81.5604113101375 2 0 0
8 101 Bmp4r Ras 1.0052953446443 889.238103252294 21 81.5604113101375 2 0 0
9 27 Actr Erk -0.327920234741696 899.875257200335 20 70.9232573620963 1 0 0
10 384 Smad2 Erk -1 899.875257200335 20 70.9232573620963 1 0 0
11 402 Stat3 Akt 0.000328137939887829 901.431902293253 20 69.3666122691785 1 1.11022302462516e-16 3.7858605139718e-14
12 220 Jak Igfr 5.55539436656802e-05 901.522264003501 20 69.2762505589305 1 1.11022302462516e-16 3.7858605139718e-14
13 409 Stat3 Igfr 0.000146754744396415 902.221664448101 20 68.5768501143306 1 1.11022302462516e-16 3.7858605139718e-14
14 408 Stat3 Gsk3 0.000160748619874925 902.324997882948 20 68.4735166794833 1 1.11022302462516e-16 3.7858605139718e-14
15 414 Stat3 Pi3k 1.17008465928704e-05 903.082143837999 20 67.7163707244331 1 2.22044604925031e-16 7.57172102794356e-14
16 219 Jak Gsk3 2.62365545377848e-05 903.256424772377 20 67.5420897900549 1 2.22044604925031e-16 7.57172102794356e-14
17 213 Jak Akt 7.21679806108667e-05 903.376234376356 20 67.4222801860755 1 2.22044604925031e-16 7.57172102794356e-14
18 225 Jak Pi3k 3.34763735789056e-06 903.440683415853 20 67.3578311465785 1 2.22044604925031e-16 7.57172102794356e-14
19 34 Actr Mek -0.143655120450202 903.646874708811 20 67.1516398536204 1 2.22044604925031e-16 7.57172102794356e-14
20 37 Actr Raf -0.143655120450202 903.646874708811 20 67.1516398536204 1 2.22044604925031e-16 7.57172102794356e-14

LA3:Bmp4r->Fgfr

Model residual = 839

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 213 Jak Akt 0.000559101694508571 776.613258315932 22 62.1769979062434 1 3.10862446895044e-15 1.05693231944315e-12
2 402 Stat3 Akt 0.00163958611575612 776.618590686197 22 62.1716655359784 1 3.10862446895044e-15 1.05693231944315e-12
3 408 Stat3 Gsk3 0.000164346770395023 778.024536203888 22 60.7657200182869 1 6.43929354282591e-15 2.18935980456081e-12
4 414 Stat3 Pi3k 0.000558220477783345 778.106835378228 22 60.683420843947 1 6.66133814775094e-15 2.26485497023532e-12
5 409 Stat3 Igfr 0.00031984920277261 778.130802407887 22 60.6594538142881 1 6.77236045021345e-15 2.30260255307257e-12
6 225 Jak Pi3k 8.97904410870197e-05 778.167767008921 22 60.6224892132536 1 6.88338275267597e-15 2.34035013590983e-12
7 226 Jak Raf -3.17320997476433 796.125380312149 22 42.6648759100262 1 6.49684750442248e-11 2.20892815150364e-08
8 223 Jak Mek -3.21824554283048 796.307860112286 22 42.4823961098889 1 7.13212822134324e-11 2.4249235952567e-08
9 227 Jak Ras -3.24588645068019 796.497908448933 22 42.292347773242 1 7.8599460273665e-11 2.67238164930461e-08
10 103 Bmp4r Smad2 100.02186644193 797.416938400438 22 41.3733178217368 1 1.25762289471254e-10 4.27591784202264e-08
11 86 Bmp4r Actr 100.010657724698 797.452728577297 22 41.3375276448785 1 1.28086097284097e-10 4.3549273076593e-08
12 27 Actr Erk -0.327920237439189 798.210046345649 22 40.5802098765256 1 1.88708271231519e-10 6.41608122187165e-08
13 384 Smad2 Erk -1 798.210046345649 22 40.5802098765256 1 1.88708271231519e-10 6.41608122187165e-08
14 118 Erk Mek -0.0986955651077006 801.650786718166 22 37.1394695040086 1 1.09975040185617e-09 3.73915136631098e-07
15 122 Erk Ras -0.0986955651090815 801.650787921435 22 37.1394683007397 1 1.09975106798998e-09 3.73915363116593e-07
16 121 Erk Raf -0.0986955651101688 801.650787967443 22 37.139468254732 1 1.09975106798998e-09 3.73915363116593e-07
17 412 Stat3 Mek -0.25107346302282 802.05483033835 22 36.7354258838252 1 1.35298316994437e-09 4.60014277781086e-07
18 416 Stat3 Ras -0.251073465040761 802.054830353862 22 36.7354258683125 1 1.35298316994437e-09 4.60014277781086e-07
19 415 Stat3 Raf -0.251073466548989 802.054830438638 22 36.7354257835368 1 1.35298316994437e-09 4.60014277781086e-07
20 220 Jak Igfr 8.04755410748596e-06 803.218989797017 22 35.5712664251585 1 2.45887887828644e-09 8.3601881861739e-07

LA4:Erk->Raf

Model residual = 798

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 213 Jak Akt 0.000707406177266371 737.960495916585 23 60.3505499670268 1 7.99360577730113e-15 2.70983235850508e-12
2 402 Stat3 Akt 0.00403762213564797 739.274618886038 23 59.0364269975745 1 1.54321000422897e-14 5.23148191433621e-12
3 220 Jak Igfr 5.03600959182369e-05 739.346387831751 23 58.964658051861 1 1.60982338570648e-14 5.45730127754497e-12
4 219 Jak Gsk3 8.91364101617684e-05 739.36887470925 23 58.9421711743623 1 1.62092561595273e-14 5.49493783807976e-12
5 414 Stat3 Pi3k 0.000701899934766581 739.373798236313 23 58.9372476472989 1 1.63202784619898e-14 5.53257439861454e-12
6 408 Stat3 Gsk3 0.000169610934882156 739.387623592905 23 58.9234222907071 1 1.64313007644523e-14 5.57021095914933e-12
7 409 Stat3 Igfr 8.16173463425947e-05 739.442288331576 23 58.8687575520361 1 1.68753899743024e-14 5.72075720128851e-12
8 225 Jak Pi3k 0.000323749018200995 739.465644562853 23 58.8454013207592 1 1.70974345792274e-14 5.79603032235809e-12
9 6 Activin Erk -0.999743480639336 760.328450472915 23 37.9825954106967 1 7.13785364148123e-10 2.41973238446214e-07
10 86 Bmp4r Actr 0.1 760.705112213975 23 37.6059336696374 1 8.65806981664718e-10 2.93508566784339e-07
11 103 Bmp4r Smad2 0.1 760.705112213975 23 37.6059336696374 1 8.65806981664718e-10 2.93508566784339e-07
12 27 Actr Erk -0.327920237444485 761.52862579633 23 36.7824200872823 1 1.32075872461002e-09 4.47737207642797e-07
13 384 Smad2 Erk -1 761.52862579633 23 36.7824200872823 1 1.32075872461002e-09 4.47737207642797e-07
14 34 Actr Mek -0.147675991438342 763.080355755634 23 35.2306901279777 1 2.92871626950131e-09 9.92834815360944e-07
15 37 Actr Raf -0.147675991438342 763.080355755634 23 35.2306901279777 1 2.92871626950131e-09 9.92834815360944e-07
16 38 Actr Ras -0.147675991438342 763.080355755634 23 35.2306901279777 1 2.92871626950131e-09 9.92834815360944e-07
17 415 Stat3 Raf -0.347655472010461 764.509160427224 23 33.8018854563885 1 6.10196959627274e-09 2.06856769313646e-06
18 416 Stat3 Ras -0.347655486454759 764.509383657584 23 33.801662226028 1 6.10266981393437e-09 2.06880506692375e-06
19 412 Stat3 Mek -0.347655508994201 764.509721078212 23 33.8013248053998 1 6.10372841158835e-09 2.06916393152845e-06
20 313 Pi3k Smad2 0.0731215380340072 765.019323945664 23 33.2917219379483 1 7.93195686910053e-09 2.68893337862508e-06

LA5:Jak->Gsk3

Model residual = 738

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 6 Activin Erk -0.999100219336439 681.894033658867 24 56.0607272911691 1 7.02771174587724e-14 2.37536657010651e-11
2 34 Actr Mek -0.169510536243249 691.497669974297 24 46.457090975739 1 9.3647312127132e-12 3.16527914989706e-09
3 37 Actr Raf -0.169510524829761 691.497670173476 24 46.4570907765599 1 9.3647312127132e-12 3.16527914989706e-09
4 38 Actr Ras -0.169510524829761 691.497670173476 24 46.4570907765599 1 9.3647312127132e-12 3.16527914989706e-09
5 384 Smad2 Erk -1.00042541472319 692.068671499042 24 45.8860894509942 1 1.25333077249934e-11 4.23625801104777e-09
6 27 Actr Erk -0.329216993650508 692.07872455242 24 45.8760363976163 1 1.25978116827241e-11 4.25806034876075e-09
7 86 Bmp4r Actr 0.1 692.718298841271 24 45.2364621087655 1 1.74623648874217e-11 5.90227933194853e-09
8 103 Bmp4r Smad2 0.1 692.718298841271 24 45.2364621087655 1 1.74623648874217e-11 5.90227933194853e-09
9 13 Activin Mek -0.102939000333209 697.615694892658 24 40.3390660573785 1 2.1349688683614e-10 7.21619477506153e-08
10 16 Activin Raf -0.102939000333209 697.615694892658 24 40.3390660573785 1 2.1349688683614e-10 7.21619477506153e-08
11 17 Activin Ras -0.102939000340934 697.61569497916 24 40.3390659708757 1 2.1349688683614e-10 7.21619477506153e-08
12 8 Activin Fgfr -0.268891542369133 697.969720461774 24 39.9850404882623 1 2.55915288960296e-10 8.64993676685801e-08
13 29 Actr Fgfr -0.931701344045143 698.398913256414 24 39.5558476936221 1 3.1881031148373e-10 1.07757885281501e-07
14 208 Igfr Smad2 0.252182901106177 703.801214372991 24 34.1535465770447 1 5.09303343942946e-09 1.72144530252716e-06
15 191 Igfr Actr 0.25201962503734 703.801382643909 24 34.153378306127 1 5.09347386490333e-09 1.72159416633733e-06
16 313 Pi3k Smad2 0.30512095678214 703.822303571833 24 34.1324573782036 1 5.14852960264989e-09 1.74020300569566e-06
17 296 Pi3k Actr 0.30512095702263 703.822303599494 24 34.1324573505418 1 5.14852960264989e-09 1.74020300569566e-06
18 187 Gsk3 Smad2 0.253667914857315 703.846862678593 24 34.1078982714434 1 5.21392051755498e-09 1.76230513493358e-06
19 170 Gsk3 Actr 0.253710860378536 703.847228684446 24 34.1075322655903 1 5.21490128857494e-09 1.76263663553833e-06
20 439 mTor Smad2 0.513028961424221 703.894000572903 24 34.0607603771336 1 5.34176891608951e-09 1.80551789363825e-06

LA6:Bmp4r->Smad2

Model residual = 692

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 6 Activin Erk -0.997740015496855 635.738196860532 25 56.1443512091877 1 6.7390537594747e-14 2.27106111694297e-11
2 27 Actr Erk -0.3764990238487 642.112873213278 25 49.7696748564417 1 1.72895031624876e-12 5.82656256575832e-10
3 13 Activin Mek -0.161779764555631 645.914166189683 25 45.9683818800364 1 1.20177201523575e-11 4.04997169134448e-09
4 16 Activin Raf -0.161779764555631 645.914166189683 25 45.9683818800364 1 1.20177201523575e-11 4.04997169134448e-09
5 17 Activin Ras -0.161779764555631 645.914166189683 25 45.9683818800364 1 1.20177201523575e-11 4.04997169134448e-09
6 384 Smad2 Erk -1.19408610007656 646.087356464795 25 45.7951916049243 1 1.31284982884949e-11 4.42430392322278e-09
7 26 Actr Bmp4r -0.114345956401805 651.432322957465 25 40.4502251122551 1 2.01689220880041e-10 6.79692674365738e-08
8 5 Activin Bmp4r -0.135186295550368 651.446998454898 25 40.4355496148218 1 2.03209782334568e-10 6.84816966467494e-08
9 34 Actr Mek -0.184466635341531 651.695610071583 25 40.1869379981371 1 2.30786167954022e-10 7.77749386005054e-08
10 37 Actr Raf -0.184466635341531 651.695610071583 25 40.1869379981371 1 2.30786167954022e-10 7.77749386005054e-08
11 38 Actr Ras -0.184466635341531 651.695610071583 25 40.1869379981371 1 2.30786167954022e-10 7.77749386005054e-08
12 29 Actr Fgfr -0.19305395874701 651.86148251821 25 40.0210655515094 1 2.51238807535969e-10 8.46674781396215e-08
13 8 Activin Fgfr -0.272144558486586 652.05207145613 25 39.8304766135902 1 2.7698909832452e-10 9.33453261353632e-08
14 194 Igfr Bmp4r 9.52513344378078 660.382834653848 25 31.4997134158713 1 1.99469695205678e-08 6.72212872843135e-06
15 173 Gsk3 Bmp4r 8.35970405891355 662.907058780043 25 28.9754892896766 1 7.32999207997409e-08 2.47020733095127e-05
16 25 Actr Bmp4 -0.0464156641394266 663.78872868241 25 28.0938193873098 1 1.15574366854609e-07 3.89485616300032e-05
17 4 Activin Bmp4 -0.0464156642277728 663.788728725367 25 28.0938193443523 1 1.15574369408122e-07 3.89485624905371e-05
18 395 Smad2 Ras -0.119503971763457 664.950226437352 25 26.9323216323673 1 2.10705583314486e-07 7.10077815769818e-05
19 394 Smad2 Raf -0.119503971643125 664.950227312366 25 26.9323207573539 1 2.10705678682643e-07 7.10078137160507e-05
20 391 Smad2 Mek -0.119503971990989 664.950227955385 25 26.9323201143351 1 2.10705748737716e-07 7.10078373246103e-05

LA7:Actr->Bmp4r

Model residual = 651

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 136 Fgf4 Igfr -0.000171702506999909 627.407489706755 26 23.7278475050618 1 1.10965255895046e-06 0.000372843259807355
2 141 Fgf4 Pi3k -9.56625374187201e-05 627.439128294579 26 23.6962089172383 1 1.12804529073252e-06 0.000379023217686127
3 129 Fgf4 Akt -0.000101035992815949 627.441534220169 26 23.6938029916479 1 1.12945639374473e-06 0.000379497348298229
4 135 Fgf4 Gsk3 -4.13969970059556e-05 627.514826205649 26 23.6205110061685 1 1.17330193050158e-06 0.000394229448648531
5 215 Jak Bmp4r 0.420445924238593 627.885090183765 26 23.2502470280523 1 1.42232177680057e-06 0.000477900117004991
6 404 Stat3 Bmp4r 0.695556761330991 628.499523263902 26 22.6358139479154 1 1.95800549551706e-06 0.000657889846493732
7 117 Erk Lifr 0.157020092622241 629.930962278401 26 21.2043749334161 1 4.12821115380879e-06 0.00138707894767975
8 264 Mek Lifr 0.508853918161392 630.02043490386 26 21.1149023079566 1 4.32551195939102e-06 0.00145337201835538
9 263 Mek Jak 0.416284621142674 630.132594660481 26 21.0027425513357 1 4.58626392585426e-06 0.00154098467908703
10 116 Erk Jak 0.117714567303387 630.144286561923 26 20.9910506498939 1 4.61433765941432e-06 0.00155041745356321
11 54 Akt Lifr 0.293890041522473 630.779454383863 26 20.3558828279544 1 6.42951189366858e-06 0.00216031599627264
12 53 Akt Jak 0.224724364896233 630.811466634632 26 20.3238705771853 1 6.53798176786236e-06 0.00219676187400175
13 282 NoLif Gsk3 0.000818038618045161 630.834893059483 26 20.300444152334 1 6.61852181327305e-06 0.00222382332925974
14 240 Lifr Gsk3 0.00135681037595657 630.852810263147 26 20.2825269486699 1 6.68079267540644e-06 0.00224474633893656
15 305 Pi3k Jak 0.573003172148801 630.867938359368 26 20.2673988524492 1 6.7338277520701e-06 0.00226256612469555
16 200 Igfr Jak 0.75580402001186 631.967408142999 26 19.1679290688176 1 1.197077927928e-05 0.00402218183783808
17 431 mTor Jak 0.996688816163702 632.060010869192 26 19.0753263426247 1 1.25659011062096e-05 0.00422214277168643
18 179 Gsk3 Jak 0.3598489800363 632.381355504872 26 18.753981706945 1 1.4871253526505e-05 0.00499674118490568
19 314 Pi3k Stat3 0.241688832998278 632.45767749664 26 18.6776597151769 1 1.54785431869531e-05 0.00520079051081624
20 62 Akt Stat3 0.0907717294756864 632.587036018461 26 18.5483011933563 1 1.65652797667892e-05 0.00556593400164117

XO

Initial-Fit

Model residual = 1604

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 218 Jak Fgfr 20.4555622071971 1087.3433154512 17 516.380135475511 1 0 0
2 407 Stat3 Fgfr 21.5653831972927 1087.34331580481 17 516.380135121903 1 0 0
3 405 Stat3 Erk 0.814942015154757 1259.70107126209 17 344.022379664625 1 0 0
4 216 Jak Erk 0.694604520012992 1259.70107127078 17 344.022379655935 1 0 0
5 223 Jak Mek 0.15351221946598 1274.91766666864 17 328.805784258074 1 0 0
6 226 Jak Raf 0.15351221946598 1274.91766666864 17 328.805784258074 1 0 0
7 227 Jak Ras 0.15351221946598 1274.91766666864 17 328.805784258074 1 0 0
8 412 Stat3 Mek 0.169230604339685 1274.91766667305 17 328.805784253661 1 0 0
9 415 Stat3 Raf 0.169230604339685 1274.91766667305 17 328.805784253661 1 0 0
10 416 Stat3 Ras 0.169230604339685 1274.91766667305 17 328.805784253661 1 0 0
11 281 NoLif Fgfr -26.1357634523209 1284.20827339087 17 319.515177535837 1 0 0
12 239 Lifr Fgfr -22.8862756816318 1284.20827339159 17 319.515177535118 1 0 0
13 237 Lifr Erk -1.09664060760853 1307.81404086072 17 295.90941006599 1 0 0
14 279 NoLif Erk -1.09664013272317 1307.81404087539 17 295.909410051324 1 0 0
15 286 NoLif Mek -0.239871655402394 1311.08678087335 17 292.63667005336 1 0 0
16 289 NoLif Raf -0.239871655402394 1311.08678087335 17 292.63667005336 1 0 0
17 290 NoLif Ras -0.239871655402394 1311.08678087335 17 292.63667005336 1 0 0
18 244 Lifr Mek -0.239871706973556 1311.08678087424 17 292.636670052469 1 0 0
19 247 Lifr Raf -0.239871706973556 1311.08678087424 17 292.636670052469 1 0 0
20 248 Lifr Ras -0.239871706973556 1311.08678087424 17 292.636670052469 1 0 0

LA1:Jak -> Fgfr

Model residual = 1064

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 118 Erk Mek -1.3134031405681 815.631614385471 18 247.924428475258 1 0 0
2 121 Erk Raf -1.3134031405681 815.631614385471 18 247.924428475258 1 0 0
3 122 Erk Ras -1.3134031405681 815.631614385471 18 247.924428475258 1 0 0
4 269 Mek Ras -5.83516557728466 815.631614406535 18 247.924428454195 1 0 0
5 268 Mek Raf -5.83501103034113 815.631614489309 18 247.92442837142 1 0 0
6 92 Bmp4r Fgfr 9.99999909080412 953.75112000258 19 109.80492285815 2 0 0
7 386 Smad2 Fgfr -0.138087505692968 960.885942418047 18 102.670100442683 1 0 0
8 8 Activin Fgfr -0.107642148736655 960.885942661641 18 102.670100199089 1 0 0
9 29 Actr Fgfr -0.107633817589381 960.885942690023 18 102.670100170707 1 0 0
10 97 Bmp4r Mek 99.9999999996109 962.159252464793 19 101.396790395936 2 0 0
11 100 Bmp4r Raf 99.9999999996109 962.159252464793 19 101.396790395936 2 0 0
12 101 Bmp4r Ras 99.9999999996109 962.159252464793 19 101.396790395936 2 0 0
13 179 Gsk3 Jak 0.109872274801102 962.880760353095 19 100.675282507635 2 0 0
14 180 Gsk3 Lifr 0.109861109481093 962.880760387493 19 100.675282473237 2 0 0
15 90 Bmp4r Erk 1.00643342523252 964.022333976477 19 99.5337088842523 2 0 0
16 27 Actr Erk -0.763289910081632 964.487926033674 18 99.0681168270553 1 0 0
17 384 Smad2 Erk -0.979127107684436 964.487926061329 18 99.0681167994004 1 0 0
18 6 Activin Erk -0.763290536507029 964.487926141927 18 99.0681167188022 1 0 0
19 391 Smad2 Mek -0.192631121143629 966.972716683902 18 96.583326176828 1 0 0
20 394 Smad2 Raf -0.192631121143629 966.972716683902 18 96.583326176828 1 0 0

LA2:Gsk3->Igfr

Model residual = 971

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 100.000000000769 869.218810406832 21 101.412816378881 2 0 0
2 97 Bmp4r Mek 100.000000005133 871.46389835036 21 99.1677284353533 2 0 0
3 100 Bmp4r Raf 100.000000005133 871.46389835036 21 99.1677284353533 2 0 0
4 101 Bmp4r Ras 100.000000005133 871.46389835036 21 99.1677284353533 2 0 0
5 90 Bmp4r Erk 100.000000093328 871.627560561552 21 99.0040662241618 2 0 0
6 27 Actr Erk -0.754763746009187 872.382026119069 20 98.2496006666448 1 0 0
7 384 Smad2 Erk -1 872.722753102278 20 97.9088736834352 1 0 0
8 13 Activin Mek -0.151274324677221 875.395343987362 20 95.2362827983517 1 0 0
9 16 Activin Raf -0.151274324677221 875.395343987362 20 95.2362827983517 1 0 0
10 17 Activin Ras -0.151274324677221 875.395343987362 20 95.2362827983517 1 0 0
11 34 Actr Mek -0.152158078351239 875.399966538021 20 95.2316602476924 1 0 0
12 37 Actr Raf -0.152158078351239 875.399966538021 20 95.2316602476924 1 0 0
13 38 Actr Ras -0.152158078351239 875.399966538021 20 95.2316602476924 1 0 0
14 6 Activin Erk -1 876.19068593168 20 94.4409408540336 1 0 0
15 29 Actr Fgfr -0.109752810948281 877.033681514489 20 93.5979452712244 1 0 0
16 8 Activin Fgfr -0.109518819568173 877.036627479454 20 93.5949993062593 1 0 0
17 386 Smad2 Fgfr -0.100000068381778 880.738339407433 20 89.8932873782805 1 0 0
18 96 Bmp4r Lifr 146.293823633502 890.206270302285 21 80.4253564834291 2 0 0
19 95 Bmp4r Jak 100.000000025193 893.519609105346 21 77.1120176803679 2 0 0
20 391 Smad2 Mek -0.1 894.495720617054 20 76.1359061686597 1 0 0

LA3:Bmp4r->Fgfr

Model residual = 867

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 268 Mek Raf -6.48420744953439 611.484728447621 22 255.595399126098 1 0 0
2 269 Mek Ras -6.48503235451705 611.486413053196 22 255.593714520524 1 0 0
3 122 Erk Ras -1.42993730891105 611.600929146642 22 255.479198427077 1 0 0
4 118 Erk Mek -1.42955753822242 611.628079213488 22 255.452048360232 1 0 0
5 121 Erk Raf -1.42912374969748 611.673124799125 22 255.407002774595 1 0 0
6 103 Bmp4r Smad2 0.875965322102496 785.739608677576 22 81.3405188961431 1 0 0
7 86 Bmp4r Actr 0.876416426590895 785.740483861214 22 81.3396437125058 1 0 0
8 359 Smad1 Actr 1 786.308377696311 22 80.771749877409 1 0 0
9 376 Smad1 Smad2 1 786.308377696828 22 80.7717498768917 1 0 0
10 149 Fgfr Actr 0.970685060228157 800.239457835563 22 66.8406697381567 1 3.33066907387547e-16 1.13242748511766e-13
11 166 Fgfr Smad2 0.970685071593034 800.239457957286 22 66.8406696164333 1 3.33066907387547e-16 1.13242748511766e-13
12 355 Ras Smad2 0.887689724088292 800.259729677718 22 66.8203978960014 1 3.33066907387547e-16 1.13242748511766e-13
13 317 Raf Actr 0.887689712593608 800.259729708413 22 66.8203978653063 1 3.33066907387547e-16 1.13242748511766e-13
14 334 Raf Smad2 0.887689699306619 800.259729744808 22 66.8203978289113 1 3.33066907387547e-16 1.13242748511766e-13
15 338 Ras Actr 0.887689698278604 800.259729746685 22 66.820397827035 1 3.33066907387547e-16 1.13242748511766e-13
16 219 Jak Gsk3 0.0954023991913973 807.47789398697 22 59.60223358675 1 1.16573417585641e-14 3.96349619791179e-12
17 408 Stat3 Gsk3 0.116250550747157 807.477895558946 22 59.6022320147737 1 1.16573417585641e-14 3.96349619791179e-12
18 113 Erk Fgfr -1.5175149811288 807.595214138194 22 59.4849134355252 1 1.23234755733392e-14 4.18998169493533e-12
19 260 Mek Fgfr -5.97670693702218 807.595214433142 22 59.484913140578 1 1.23234755733392e-14 4.18998169493533e-12
20 110 Erk Bmp4r -0.000225633437653167 807.599122894852 22 59.4810046788676 1 1.23234755733392e-14 4.18998169493533e-12

LA4:Erk->Raf

Model residual = 611

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 86 Bmp4r Actr 1 538.054691994744 23 73.4266896923361 1 0 0
2 103 Bmp4r Smad2 1 538.054691994744 23 73.4266896923361 1 0 0
3 338 Ras Actr 0.972501250488619 545.487280932185 23 65.9941007548952 1 4.44089209850063e-16 1.50546242139171e-13
4 355 Ras Smad2 0.972436848502515 545.489382476489 23 65.9919992105911 1 4.44089209850063e-16 1.50546242139171e-13
5 408 Stat3 Gsk3 0.11645328055495 547.331781154314 23 64.1496005327663 1 1.11022302462516e-15 3.76365605347929e-13
6 219 Jak Gsk3 0.097227252336912 547.331783332299 23 64.1495983547812 1 1.11022302462516e-15 3.76365605347929e-13
7 414 Stat3 Pi3k 0.00223319697700812 550.103433577891 23 61.3779481091896 1 4.66293670342566e-15 1.5807355424613e-12
8 225 Jak Pi3k 0.00814337884241785 550.116268160372 23 61.3651135267081 1 4.77395900588817e-15 1.61837210299609e-12
9 220 Jak Igfr 0.00147940987131239 550.139649856149 23 61.3417318309314 1 4.77395900588817e-15 1.61837210299609e-12
10 409 Stat3 Igfr 0.00133333310152612 550.150826676615 23 61.3305550104649 1 4.77395900588817e-15 1.61837210299609e-12
11 213 Jak Akt 0.000326884318160387 550.170695575493 23 61.310686111587 1 4.88498130835069e-15 1.65600866353088e-12
12 402 Stat3 Akt 0.000681745589889224 550.173491284069 23 61.3078904030116 1 4.88498130835069e-15 1.65600866353088e-12
13 149 Fgfr Actr 0.999999999999996 551.103681406195 23 60.3777002808851 1 7.88258347483861e-15 2.67219579797029e-12
14 166 Fgfr Smad2 0.999999999999996 551.103681406195 23 60.3777002808849 1 7.88258347483861e-15 2.67219579797029e-12
15 107 Erk Actr 0.126706984182453 552.877015400509 23 58.6043662865713 1 1.93178806284777e-14 6.54876153305394e-12
16 124 Erk Smad2 0.126697788192819 552.877929597554 23 58.6034520895264 1 1.93178806284777e-14 6.54876153305394e-12
17 254 Mek Actr 0.59438460540211 552.893586778656 23 58.5877949084241 1 1.94289029309402e-14 6.58639809358873e-12
18 271 Mek Smad2 0.594390267384607 552.894447059316 23 58.5869346277639 1 1.94289029309402e-14 6.58639809358873e-12
19 415 Stat3 Raf -5.39253521231173 553.106579027843 23 58.3748026592369 1 2.16493489801906e-14 7.33912930428461e-12
20 227 Jak Ras -4.20013840049262 553.491954053355 23 57.9894276337252 1 2.63122856836162e-14 8.91986484674589e-12

LA5:Jak ->Gsk3

Model residual = 547

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 86 Bmp4r Actr 1.34506065680717 465.989068796561 24 81.34271123274 1 0 0
2 103 Bmp4r Smad2 1.34504409171201 465.989068797419 24 81.3427112318826 1 0 0
3 376 Smad1 Smad2 1 465.989068824412 24 81.3427112048893 1 0 0
4 359 Smad1 Actr 1 465.989068827716 24 81.3427112015858 1 0 0
5 166 Fgfr Smad2 0.787374824949833 487.061033975627 24 60.270746053674 1 8.21565038222616e-15 2.77688982919244e-12
6 338 Ras Actr 0.787455359343572 487.061033993199 24 60.2707460361019 1 8.21565038222616e-15 2.77688982919244e-12
7 355 Ras Smad2 0.787502733552122 487.061034044346 24 60.2707459849557 1 8.21565038222616e-15 2.77688982919244e-12
8 149 Fgfr Actr 0.787361722517166 487.061034176801 24 60.2707458525001 1 8.21565038222616e-15 2.77688982919244e-12
9 254 Mek Actr 0.543845407260371 493.382475651737 24 53.9493043775648 1 2.05724326463042e-13 6.95348223445082e-11
10 271 Mek Smad2 0.543845594194931 493.382475743574 24 53.9493042857273 1 2.05724326463042e-13 6.95348223445082e-11
11 107 Erk Actr 0.123251772849866 493.382475913176 24 53.9493041161249 1 2.05724326463042e-13 6.95348223445082e-11
12 124 Erk Smad2 0.123252011763697 493.382475950772 24 53.9493040785295 1 2.05724326463042e-13 6.95348223445082e-11
13 179 Gsk3 Jak 0.254057940252951 498.90101774214 24 48.4307622871614 1 3.42159633959227e-12 1.15649956278219e-09
14 180 Gsk3 Lifr 0.254068705210873 498.901018202538 24 48.4307618267629 1 3.42159633959227e-12 1.15649956278219e-09
15 200 Igfr Jak 0.39468277779385 502.069366179668 24 45.2624138496332 1 1.72324376990218e-11 5.82456394226937e-09
16 201 Igfr Lifr 0.394481641402181 502.06936628535 24 45.262413743951 1 1.72324376990218e-11 5.82456394226937e-09
17 8 Activin Fgfr -0.0929446875223427 502.642865707683 24 44.6889143216187 1 2.30960806035796e-11 7.8064752440099e-09
18 29 Actr Fgfr -0.0929454245928924 502.642865730224 24 44.6889142990776 1 2.30960806035796e-11 7.8064752440099e-09
19 386 Smad2 Fgfr -0.119228947142523 502.642865778709 24 44.6889142505922 1 2.30960806035796e-11 7.8064752440099e-09
20 383 Smad2 Bmp4r -0.000503740399463089 502.643770899251 24 44.68800913005 1 2.31068497669185e-11 7.81011522121845e-09

LA6:Bmp4r->Smad2

Model residual = 466

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 180 Gsk3 Lifr 0.254065052403451 417.558306751425 25 48.4307620559355 1 3.42159633959227e-12 1.15307796644259e-09
2 179 Gsk3 Jak 0.254066047918223 417.558306885212 25 48.4307619221488 1 3.42159633959227e-12 1.15307796644259e-09
3 200 Igfr Jak 0.394692223232032 420.726654328766 25 45.2624144785951 1 1.72324376990218e-11 5.80733150457035e-09
4 201 Igfr Lifr 0.394595483955924 420.726654602669 25 45.2624142046917 1 1.72324376990218e-11 5.80733150457035e-09
5 29 Actr Fgfr -0.0929448139068522 421.300154434767 25 44.6889143725937 1 2.30960806035796e-11 7.78337916340632e-09
6 386 Smad2 Fgfr -0.0994359792194196 421.300154441298 25 44.6889143660631 1 2.30960806035796e-11 7.78337916340632e-09
7 8 Activin Fgfr -0.0929473638282564 421.300154452023 25 44.6889143553376 1 2.30960806035796e-11 7.78337916340632e-09
8 383 Smad2 Bmp4r -6.6538659223381e-05 421.301339789439 25 44.6877290179215 1 2.31100694136899e-11 7.7880933924135e-09
9 382 Smad2 Bmp4 1 421.3013402415 25 44.6877285658604 1 2.31100694136899e-11 7.7880933924135e-09
10 26 Actr Bmp4r -0.000140141598918061 421.302820080091 25 44.6862487272697 1 2.3127610937479e-11 7.79400488593042e-09
11 25 Actr Bmp4 -0.00014013479222055 421.302822167555 25 44.686246639806 1 2.3127610937479e-11 7.79400488593042e-09
12 4 Activin Bmp4 -0.000140135265512838 421.302822175243 25 44.686246632118 1 2.3127610937479e-11 7.79400488593042e-09
13 5 Activin Bmp4r -0.000140143616979495 421.302822295164 25 44.6862465121964 1 2.3127610937479e-11 7.79400488593042e-09
14 394 Smad2 Raf -0.823997710128468 422.178358548019 25 43.8107102593414 1 3.61720653430098e-11 1.21899860205943e-08
15 395 Smad2 Ras -0.823997776732209 422.178358549224 25 43.8107102581371 1 3.61720653430098e-11 1.21899860205943e-08
16 391 Smad2 Mek -0.823997262369139 422.178358550684 25 43.8107102566772 1 3.61720653430098e-11 1.21899860205943e-08
17 13 Activin Mek -0.766281802333446 422.577980559772 25 43.4110882475888 1 4.43667325100705e-11 1.49515888558938e-08
18 16 Activin Raf -0.766281802333446 422.577980559772 25 43.4110882475888 1 4.43667325100705e-11 1.49515888558938e-08
19 17 Activin Ras -0.766281802333446 422.577980559772 25 43.4110882475888 1 4.43667325100705e-11 1.49515888558938e-08
20 34 Actr Mek -0.766282409199382 422.5779805724 25 43.411088234961 1 4.43667325100705e-11 1.49515888558938e-08

LA7:Actr->Bmp4r

Model residual = 421

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 180 Gsk3 Lifr 0.198638973271869 385.047283318677 26 36.25473399488 1 1.73138925418925e-09 5.81746789407588e-07
2 179 Gsk3 Jak 0.198636048215218 385.047294407416 26 36.2547229061416 1 1.73139913517417e-09 5.81750109418521e-07
3 188 Gsk3 Stat3 0.155300697027229 387.3530474701 26 33.9489698434573 1 5.65766333782136e-09 1.90097488150798e-06
4 201 Igfr Lifr 0.348512997176483 388.891352120685 26 32.4106651928718 1 1.24799656164853e-08 4.19326844713906e-06
5 200 Igfr Jak 0.3485124279963 388.891354814541 26 32.410662499016 1 1.24799828249422e-08 4.19327422918058e-06
6 209 Igfr Stat3 0.248199280468535 392.773026133605 26 28.5289911799522 1 9.23059626511957e-08 3.10148034508018e-05
7 234 Lifr Akt 0.0465599314232042 395.083809486956 26 26.218207826601 1 3.04933785444383e-07 0.000102457751909313
8 276 NoLif Akt 0.0465600006314084 395.083857290837 26 26.2181600227203 1 3.04941334072772e-07 0.000102460288248451
9 241 Lifr Igfr 0.134000793526346 395.630083197019 26 25.671934116538 1 4.04669677656067e-07 0.000135969011692439
10 283 NoLif Igfr 0.134140540681871 395.630097546065 26 25.6719197674927 1 4.04672686582508e-07 0.000135970022691723
11 246 Lifr Pi3k 137.800332148298 395.7374828565 26 25.5645344570572 1 4.27831139848678e-07 0.000143751262989156
12 288 NoLif Pi3k 133.859965121113 395.737486643141 26 25.5645306704158 1 4.27831979510351e-07 0.000143751545115478
13 240 Lifr Gsk3 0.122823623661381 395.921691108318 26 25.3803262052391 1 4.70694108578584e-07 0.000158153220482404
14 282 NoLif Gsk3 0.122821863643751 395.921738752211 26 25.380278561346 1 4.70705733834897e-07 0.000158157126568525
15 54 Akt Lifr 0.56618882474856 397.020494865756 26 24.2815224478009 1 8.32336903400233e-07 0.000279665199542478
16 431 mTor Jak 0.465337458856917 397.020496692259 26 24.2815206212979 1 8.32337692657781e-07 0.000279665464733014
17 432 mTor Lifr 0.465338156421058 397.020501062787 26 24.2815162507699 1 8.32339581258168e-07 0.000279666099302744
18 53 Akt Jak 0.566149713542637 397.020501600915 26 24.2815157126425 1 8.32339813849892e-07 0.000279666177453564
19 305 Pi3k Jak 0.00173202223928323 397.020638990924 26 24.2813783226333 1 8.32399185357602e-07 0.000279686126280154
20 306 Pi3k Lifr 0.000622528208386818 397.020652026436 26 24.281365287121 1 8.32404818740251e-07 0.000279688019096724

Summary

Links Added and Residuals

Model_iteration Links res_p_001_XX res_p_001_XO
1 Init Init Network 2056.3 1603.72
2 1 Jak->Fgfr 1515 1063.56
3 2 Gsk3->Igfr 970.8 970.63
4 3 Bmp4r->Fgfr 838.79 867.08
5 4 Erk->Raf 798.31 611.48
6 5 Jak->Gsk3 737.95 547.33
7 6 Bmp4r->Smad2 691.88 465.99
8 7 Actr->Bmp4r 651.14 421.3